The mathematical model of the principal axis control system of variable vector propeller of submersible vehicle is built. Because of the uncertainty of moment of inertia and damping coefficient, the control system may not achieve expected optimal performance, even causing instability. In accordance with these problems, the model reference adaptive fuzzy PID (Proportional Integration Differential) control system is designed in this paper. This system firstly analyses the factors of moment of inertia and damping coefficient, using the error and the error rate of model reference's speed and practical speed as input, and then the system adjusts the PID parameters respectively in real-time way using the adaptive fuzzy PID controller. The result of system simulation show that the system present in this paper has better adaptive ability to achieve the expected optimal performance compared with the PID control system and the proposed adaptive fuzzy PID control strategy can improve the system robustness.